LOCUS       NZ_CP062894             4286 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli O100:H21 strain Res13-Lact-ER07-18 plasmid
            unnamednovel_0, complete sequence.
ACCESSION   NZ_CP062894
VERSION     NZ_CP062894.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16304150
            Assembly: GCF_015571795.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O100:H21
  ORGANISM  Escherichia coli O100:H21
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4286)
  AUTHORS   Poulin-Laprade,D., Brouard,J.-S., Gagnon,N., Turcotte,A.,
            Langlois,A., Matte,J.J., Carrillo,C.D., Zaheer,R., McAllister,T.,
            Topp,E. and Talbot,G.
  TITLE     Resistance determinants and their genetic context in bacteria from a
            longitudinal study of pigs reared under conventional and
            antibiotic-free husbandry practices
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4286)
  AUTHORS   Poulin-Laprade,D. and Brouard,J.-S.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-SEP-2020) Sciences and Technology, Agriculture and
            Agri-Food Canada, 2000 College, Sherbrooke, Quebec J1M 0C8, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 23-NOV-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: QIA-21-A
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 1.00x
            Sequencing Technology :: Oxford Nanopore MinION and Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/16/2023 13:28:07
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,811
            CDSs (total)                      :: 4,688
            Genes (coding)                    :: 4,494
            CDSs (with protein)               :: 4,494
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 194
            CDSs (without protein)            :: 194
            Pseudo Genes (ambiguous residues) :: 0 of 194
            Pseudo Genes (frameshifted)       :: 67 of 194
            Pseudo Genes (incomplete)         :: 135 of 194
            Pseudo Genes (internal stop)      :: 32 of 194
            Pseudo Genes (multiple problems)  :: 37 of 194
            Pseudo Genes (short protein)      :: 2 of 194
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062894.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..4286
                     /organism="Escherichia coli O100:H21"
                     /mol_type="genomic DNA"
                     /strain="Res13-Lact-ER07-18"
                     /serotype="O100:H21"
                     /isolation_source="feces"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:2778652"
                     /plasmid="unnamednovel_0"
                     /geo_loc_name="Canada: Quebec"
                     /collection_date="2017-03-20"
                     /collected_by="Agriculture and Agri-Food Canada"
     gene            complement(join(3335..4286,1..59))
                     /locus_tag="IMP41_RS23825"
                     /old_locus_tag="IMP41_23820"
     CDS             complement(join(3335..4286,1..59))
                     /locus_tag="IMP41_RS23825"
                     /old_locus_tag="IMP41_23820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000395670.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001522447.1"
                     /translation="MEFQELENSACLYWPKELAERAASISAISPLIETQDEFLSILTIS
                     TNKPTSCFDAVRLCNKISPNLFVKHLMVLSDIGGERLHRFFKDLDKIYPDRIMEFNIGN
                     NSYSYQFNSNRAWTTKNLNVEKSRLLQPVSDFTREMLDVCMLILWGGNTINNTNLPTEI
                     ENNCILGNLIGNKEAIEQFVKERYIMVSRQTGGATANDLGHICEIFIKEKLYKLIDDNI
                     SLDGHHIDGVTHNDKDLTTFDIVAKNTITKKCVGIEISFQVTTNSTIERKAGLAKSRRD
                     LLNSIGHKIAYVIDGSGNFQRSNAIKTIINHSDMTVNFSDNGINSLATFICETLK"
                     /name="hypothetical protein"
     gene            complement(1082..1276)
                     /locus_tag="IMP41_RS23835"
                     /old_locus_tag="IMP41_23830"
     CDS             complement(1082..1276)
                     /locus_tag="IMP41_RS23835"
                     /old_locus_tag="IMP41_23830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2091..3338)
                     /locus_tag="IMP41_RS23840"
                     /old_locus_tag="IMP41_23835"
     CDS             complement(2091..3338)
                     /locus_tag="IMP41_RS23840"
                     /old_locus_tag="IMP41_23835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001522448.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_001522448.1"
                     /translation="MIKFVDLFSGTGGIRLGFEQAMKEIGLSTKCVKSSEIDKKACETY
                     KLNFDEESYCDIHDVDIDESFDVLLAGFPCQAFSYAGKQLGFADTRGTLFFEVERIIKK
                     NKPKLCLLENVRGLTSHDKGRTFSTILKSLHDLGYHVEYRLLNTSNFGVPQNRVRIYII
                     ASLKKEVTLTIPNDLGAKDTHNYKPSKGGHDFYTESKVSDILEDSPDKSYDCSDWFKQR
                     LEDIFKGDLNKVHGIRLIDTRNGNSLHSWDLGLKGECSNDEIAFMNSLIANRRKHIFGT
                     HQDGKALSKAQIETFFKHSETTNIIKNLIKKGYLKEKNGLYNPVCGNMSFEVFKFLDPN
                     KVSITLTASDANRLGVYHNNRLRRLTPRECARLQGYPDSYILHPKDSMAYKQLGNAVSV
                     PVIKNIFLDIMKNNFI"
                     /name="DNA cytosine methyltransferase"
     Typing          917..1002
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.851"
                     /coverage="100.0"
                     /evalue="3.99e-36"
     Typing          1313..1411
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          1536..1791
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.899"
                     /coverage="89.0"
                     /evalue="2.61e-118"
     Typing          complement(347..895)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.414"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tctgcaagtt ctttgggcca gtataagcat gcgctatttt ctaattcttg gaactccatg
       61 attattcctt ggtaaaacta tccaaataga ccttgagtta cacccctatg atgggtaatc
      121 tctacgggcg taaacgaaaa aacccacgtt ctcaggcgtg ggtttttcga aggttagaag
      181 tttctcaggc tttctaaccc aaggtaacag ggcgtacaag accgctgcca ccaaatctgt
      241 cctttcagtg tagccgcagt cgggccttca cttcaagaac tccgtatcag caatttcttg
      301 tacaccctct accaatggct gctgccagtg gtgcttttgc atgtctttcc gggttggact
      361 caagacgaca gttaccggat aaggcgcagc ggtcgggctg aacggggggt tcgtgcacac
      421 agcccagctt ggagcgaacg acctacaccg aactgagata ccaacagcgt gagctatgag
      481 aaagcgccac gcttcccgaa gggagaaagg cggacaggta tccggtaagc ggcagggtcg
      541 gaacaggaga gcgcacgagg gagcttccag ggggaaacgc ctggtatctt tatagtcctg
      601 tcgggtttcg ccacctctga cttgagcgtc ggtttttgtg atgctcgtca ggggggcgga
      661 gcctatggaa aaacgccagc ggcgtggcct tttccgggtt ctcgtttttt gctcacatgt
      721 ttcttttggc gttatcccct gattctgtgg ataaccgcat ctccgctttt gagtgagccg
      781 acaccgctcg ccgcagccga acgaccgagc gtagcgagtc agtgagcgag gaagcggaag
      841 agcgccggaa cgtgcatttt ctccttacgc atctgtgcgg catttcacac cgcatatggc
      901 gctcttttct tacaatctgc actgatgccg catggttaag tcagtataca ctccgctatc
      961 gctacgtgac tgggtcatgg ctgcgccccg acacccgcta aaaccccctg acgcgccctg
     1021 acgggcttgt ctgctgacga aaacgcccac gggaaagccg tgaccgcctc cgtcagcttc
     1081 gttatgttcc tgtttcactt tcggcctcaa agcgaatctg gatgctgttc tggagttctt
     1141 ctgcgagttc gtgcagtcgt tcgcacatgg ccgcctgttc gtcggcatcc agagcatcca
     1201 gtttttcaag cagtgtcagg ctctggcttt tgataaatcg cgccatattc agcgcagttt
     1261 gttgttgttt gttcaccttc cgttgttctc cgtcagttcc gggtgtcggg gggaccctga
     1321 gcaggtggta attgtaagac gttgcgggcg acggtattac aattgcacat cctgtcctgt
     1381 ttctttagga cgtatcatgg cacagcatat caactgataa ataatccctg tgcagtgcag
     1441 ccgctgttgc ataaaatttc gctctgcgtc gagtgtttct taatcaataa ttccgctgat
     1501 actccggaaa aacgcgagtc tgttctcatg cctgaaatgc ccacacccca cgcaaaaaca
     1561 agtttttgct gatttttctt tataaataga gagttatgac aaattagttc ttcttgctct
     1621 ctttgtgata tttaaaaaag cggtgtcggc gcggtgttgt agctgcgcca acaccgcttt
     1681 ttaggggtgg tactgactat tttcataaaa aacatcatct tatattaggg gtgctgctag
     1741 cggcgcggtg tgttttttta caggacaccc ctgggggcgc tgctaggggt gtctgttcag
     1801 atatgtagca atgagtcagg gattcacgaa ctgaaaatgt ccgaaaatgt gtctcatggg
     1861 cactgtatgc gcccaaaccg atcgtcattc actttcatgc atagctatgc agtgagctga
     1921 aagcgatcct gacgcatttt tccggtttac cccggggaga acatctcttt ttgcggtgtt
     1981 cgcggcagaa tcgctttcag cgcgttttag cggtgcgcgc aatgcgacat tatggtaaat
     2041 ctgttaaatt taattaaata accatagagc agttttgcta gtaatatagt ttatatgaag
     2101 ttattcttca ttatatcaag aaaaatattt ttaatgactg gaacgcttac agcattcccc
     2161 aattgtttat atgccatgct atcttttggg tgtaagatat atgagtctgg gtaaccttgt
     2221 agccttgcac attctcttgg tgtaaggcgt cgcagtctat tgttgtgata gactccaagt
     2281 ctattggcat cagatgcagt aagtgtaatt gacactttat ttgggtcaag gaatttgaat
     2341 acttcaaaag acatatttcc gcaaactggg ttgtatagtc cgtttttttc tttaaggtaa
     2401 ccctttttaa ttagattttt tattatgttg gtggtttcgc tatgtttgaa aaatgtttca
     2461 atttgtgctt ttgacaaagc cttgccgtct tggtgtgtgc caaaaatatg ctttctacga
     2521 tttgcaatta atgaattcat gaaagctatt tcatcatttg agcactcgcc ttttagccca
     2581 agatcccaag agtgcaagga gttgccgttc cttgtgtcaa ttagcctgat tccatgaact
     2641 ttattcaggt cacctttaaa aatatcttca aggcgttgct tgaaccaatc gctgcaatca
     2701 tatgacttgt ctggactatc ctctagtatg tcagaaactt ttgattctgt ataaaaatca
     2761 tgaccacctt tggatggttt gtaattgtgc gtatctttgg ctccaagatc attaggaata
     2821 gtaagcgtta cctctttttt taatgaggct attatatata ttctaaccct attttgaggg
     2881 acgccaaaat tacttgtatt taatagtctg tattcaacat gataccctaa atcgtgaagg
     2941 gattttaata ttgttgaaaa tgtccttcct ttatcatgtg aagttaatcc acgtacattc
     3001 tccaaaagac acaatttagg cttgtttttc tttataattc tttctacttc aaaaaataat
     3061 gtacctcggg tgtctgcaaa accaagttgt tttccagcat aagagaatgc ttggcaagga
     3121 aatcctgcca ataaaacatc gaagctttca tctatatcaa catcatgtat atcacaatat
     3181 gattcttcgt cgaagttaag tttgtatgtt tcgcatgctt ttttgtcaat ttctgagctt
     3241 tttacacatt ttgttgacaa tccaatttct ttcatggctt gctcaaaacc aagtctaata
     3301 ccacctgtgc cagaaaaaag gtcaacaaat ttaatcattt caatgtctcg cagatgaatg
     3361 ttgctagtga atttatacca ttatctgaaa agttaacagt catgtcacta tggttaatta
     3421 ttgtttttat ggcatttgag cgctgaaaat taccagaccc atcaatcaca tatgctattt
     3481 tatgccctat tgaattgagt aaatctcttc tgcttttggc taatcctgct tttctttcta
     3541 ttgttgagtt tgttgtaact tgaaaactta tttcaatacc aacacatttt tttgttatcg
     3601 tgttttttgc tacaatatca aaagtcgtaa ggtctttatc gttatgagtt acaccatcga
     3661 tatggtgtcc atctagagat atattatcat caataagttt ataaagtttt tcttttataa
     3721 agatctcgca tatgtgtcca agatcatttg ccgttgcacc tcctgtttgt ctgctaacca
     3781 ttatatatct ttcttttaca aattgttcta ttgcttcttt gttcccaatt aaatttccca
     3841 aaatacagtt attttctatt tcagttggaa ggtttgtatt gtttatagtg ttacctcccc
     3901 acaggatcag catgcaaaca tcaagcattt ctcgtgtaaa atcacttaca ggttgcaaaa
     3961 gtcgtgattt ttccacgttt aaattcttgg ttgtccatgc tctattgcta ttgaattggt
     4021 aagagtaaga gttattccct atattgaact ccattattct gtcaggatag attttatcta
     4081 aatctttaaa aaagcgatga agtctttcgc ctccaatatc tgacaaaacc attaggtgct
     4141 tgacaaatag gttgggtgat atcttattgc ataaccgtac agcatcaaaa caagatgtag
     4201 gcttatttgt tgatattgtt agtattgata aaaattcatc ttgggtctct ataagagggc
     4261 ttatggcgct aatagatgct gctctt
//
